def _processParameterNode(self, parameterNode):
if not self.registrationResult:
self.registrationResult = RegistrationResult("01: RegistrationResult")
result = self.registrationResult
result.fixedVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedImageNodeID'))
result.fixedLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedLabelNodeID'))
result.movingLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingLabelNodeID'))
movingVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingImageNodeID'))
result.movingVolume = self.volumesLogic.CloneVolume(slicer.mrmlScene, movingVolume, "temp-movingVolume_" + str(self.counter))
self.counter += 1
logging.debug("Fixed Image Name: %s" % result.fixedVolume.GetName())
logging.debug("Fixed Label Name: %s" % result.fixedLabel.GetName())
logging.debug("Moving Image Name: %s" % movingVolume.GetName())
logging.debug("Moving Label Name: %s" % result.movingLabel.GetName())
initialTransform = parameterNode.GetAttribute('InitialTransformNodeID')
if initialTransform:
initialTransform = slicer.mrmlScene.GetNodeByID(initialTransform)
logging.debug("Initial Registration Name: %s" % initialTransform.GetName())
return result
def runReRegistration(self, parameterNode, progressCallback=None):
self.progressCallback = progressCallback
registrationTypes = ['rigid', 'bSpline']
if not self.registrationResult:
self.registrationResult = RegistrationResult("01: RegistrationResult")
result = self.registrationResult
result.fixedVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedImageNodeID'))
fixedLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedLabelNodeID'))
result.fixedLabel = self.volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, result.fixedVolume,
result.fixedVolume.GetName() + '-label')
result.movingLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingLabelNodeID'))
movingVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingImageNodeID'))
result.movingVolume = self.volumesLogic.CloneVolume(slicer.mrmlScene, movingVolume, "temp-movingVolume")
self.createVolumeAndTransformNodes(registrationTypes, prefix=str(result.seriesNumber), suffix=result.suffix)
initialTransform = parameterNode.GetAttribute('InitialTransformNodeID')
if initialTransform:
initialTransform = slicer.mrmlScene.GetNodeByID(initialTransform)
self.runBRAINSResample(inputVolume=fixedLabel, referenceVolume=result.fixedVolume, outputVolume=result.fixedLabel,
warpTransform=initialTransform)
if initialTransform:
self.doRigidRegistration(movingBinaryVolume=result.movingLabel, initialTransform=initialTransform)
else:
self.doRigidRegistration(movingBinaryVolume=result.movingLabel)
self.dilateMask(result.fixedLabel)
self.doBSplineRegistration(initialTransform=result.rigidTransform, useScaleVersor3D=True,
useScaleSkewVersor3D=True, useAffine=True)
targetsNodeID = parameterNode.GetAttribute('TargetsNodeID')
if targetsNodeID:
result.originalTargets = slicer.mrmlScene.GetNodeByID(targetsNodeID)
self.transformTargets(registrationTypes, result.originalTargets, str(result.seriesNumber), suffix=result.suffix)
result.movingVolume = movingVolume
def run(self, parameterNode, progressCallback=None):
self.progressCallback = progressCallback
registrationTypes = ['rigid', 'affine', 'bSpline']
if not self.registrationResult:
self.registrationResult = RegistrationResult("01: RegistrationResult")
result = self.registrationResult
result.fixedVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedImageNodeID'))
result.fixedLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedLabelNodeID'))
result.movingLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingLabelNodeID'))
movingVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingImageNodeID'))
result.movingVolume = self.volumesLogic.CloneVolume(slicer.mrmlScene, movingVolume, "temp-movingVolume")
self.createVolumeAndTransformNodes(registrationTypes, prefix=str(result.seriesNumber), suffix=result.suffix)
self.doRigidRegistration(movingBinaryVolume=result.movingLabel, initializeTransformMode="useCenterOfROIAlign")
self.doAffineRegistration()
self.doBSplineRegistration(initialTransform=result.affineTransform)
targetsNodeID = parameterNode.GetAttribute('TargetsNodeID')
if targetsNodeID:
result.originalTargets = slicer.mrmlScene.GetNodeByID(targetsNodeID)
self.transformTargets(registrationTypes, result.originalTargets, str(result.seriesNumber), suffix=result.suffix)
result.movingVolume = movingVolume
class SliceTrackerRegistrationLogic(ScriptedLoadableModuleLogic, ModuleLogicMixin):
counter = 1
def __init__(self):
ScriptedLoadableModuleLogic.__init__(self)
self.volumesLogic = slicer.modules.volumes.logic()
self.markupsLogic = slicer.modules.markups.logic()
self.registrationResult = None
def _processParameterNode(self, parameterNode):
if not self.registrationResult:
self.registrationResult = RegistrationResult("01: RegistrationResult")
result = self.registrationResult
result.fixedVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedImageNodeID'))
result.fixedLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('FixedLabelNodeID'))
result.movingLabel = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingLabelNodeID'))
movingVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingImageNodeID'))
result.movingVolume = self.volumesLogic.CloneVolume(slicer.mrmlScene, movingVolume, "temp-movingVolume_" + str(self.counter))
self.counter += 1
logging.debug("Fixed Image Name: %s" % result.fixedVolume.GetName())
logging.debug("Fixed Label Name: %s" % result.fixedLabel.GetName())
logging.debug("Moving Image Name: %s" % movingVolume.GetName())
logging.debug("Moving Label Name: %s" % result.movingLabel.GetName())
initialTransform = parameterNode.GetAttribute('InitialTransformNodeID')
if initialTransform:
initialTransform = slicer.mrmlScene.GetNodeByID(initialTransform)
logging.debug("Initial Registration Name: %s" % initialTransform.GetName())
return result
def run(self, parameterNode, progressCallback=None):
self.progressCallback = progressCallback
result = self._processParameterNode(parameterNode)
registrationTypes = ['rigid', 'affine', 'bSpline']
self.createVolumeAndTransformNodes(registrationTypes, prefix=str(result.seriesNumber), suffix=result.suffix)
self.doRigidRegistration(movingBinaryVolume=result.movingLabel, initializeTransformMode="useCenterOfROIAlign")
self.doAffineRegistration()
self.doBSplineRegistration(initialTransform=result.affineTransform)
targetsNodeID = parameterNode.GetAttribute('TargetsNodeID')
if targetsNodeID:
result.originalTargets = slicer.mrmlScene.GetNodeByID(targetsNodeID)
self.transformTargets(registrationTypes, result.originalTargets, str(result.seriesNumber), suffix=result.suffix)
result.movingVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingImageNodeID'))
def runReRegistration(self, parameterNode, progressCallback=None):
logging.debug("Starting Re-Registration")
self.progressCallback = progressCallback
self._processParameterNode(parameterNode)
result = self.registrationResult
registrationTypes = ['rigid', 'bSpline']
self.createVolumeAndTransformNodes(registrationTypes, prefix=str(result.seriesNumber), suffix=result.suffix)
initialTransform = parameterNode.GetAttribute('InitialTransformNodeID')
if initialTransform:
initialTransform = slicer.mrmlScene.GetNodeByID(initialTransform)
# TODO: label value should be delivered by parameterNode
self.dilateMask(result.fixedLabel, dilateValue=8)
self.doRigidRegistration(movingBinaryVolume=result.movingLabel,
initialTransform=initialTransform if initialTransform else None)
self.doBSplineRegistration(initialTransform=result.rigidTransform, useScaleVersor3D=True, useScaleSkewVersor3D=True,
useAffine=True)
targetsNodeID = parameterNode.GetAttribute('TargetsNodeID')
if targetsNodeID:
result.originalTargets = slicer.mrmlScene.GetNodeByID(targetsNodeID)
self.transformTargets(registrationTypes, result.originalTargets, str(result.seriesNumber), suffix=result.suffix)
result.movingVolume = slicer.mrmlScene.GetNodeByID(parameterNode.GetAttribute('MovingImageNodeID'))
def createVolumeAndTransformNodes(self, registrationTypes, prefix, suffix=""):
for regType in registrationTypes:
self.registrationResult.setVolume(regType, self.createScalarVolumeNode(prefix + '-VOLUME-' + regType + suffix))
transformName = prefix + '-TRANSFORM-' + regType + suffix
transform = self.createBSplineTransformNode(transformName) if regType == 'bSpline' \
else self.createLinearTransformNode(transformName)
self.registrationResult.setTransform(regType, transform)
def transformTargets(self, registrations, targets, prefix, suffix=""):
if targets:
for registration in registrations:
name = prefix + '-TARGETS-' + registration + suffix
clone = self.cloneFiducialAndTransform(name, targets, self.registrationResult.getTransform(registration))
self.markupsLogic.SetAllMarkupsLocked(clone, True)
self.registrationResult.setTargets(registration, clone)
def cloneFiducialAndTransform(self, cloneName, originalTargets, transformNode):
tfmLogic = slicer.modules.transforms.logic()
clonedTargets = self.cloneFiducials(originalTargets, cloneName)
clonedTargets.SetAndObserveTransformNodeID(transformNode.GetID())
tfmLogic.hardenTransform(clonedTargets)
return clonedTargets
def doRigidRegistration(self, **kwargs):
self.updateProgress(labelText='\nRigid registration', value=2)
paramsRigid = {'fixedVolume': self.registrationResult.fixedVolume,
'movingVolume': self.registrationResult.movingVolume,
'fixedBinaryVolume': self.registrationResult.fixedLabel,
'outputTransform': self.registrationResult.rigidTransform.GetID(),
'outputVolume': self.registrationResult.rigidVolume.GetID(),
'maskProcessingMode': "ROI",
'useRigid': True}
for key, value in kwargs.iteritems():
paramsRigid[key] = value
slicer.cli.run(slicer.modules.brainsfit, None, paramsRigid, wait_for_completion=True)
self.registrationResult.cmdArguments += "Rigid Registration Parameters: %s" % str(paramsRigid) + "\n\n"
def doAffineRegistration(self):
self.updateProgress(labelText='\nAffine registration', value=2)
paramsAffine = {'fixedVolume': self.registrationResult.fixedVolume,
'movingVolume': self.registrationResult.movingVolume,
'fixedBinaryVolume': self.registrationResult.fixedLabel,
'movingBinaryVolume': self.registrationResult.movingLabel,
'outputTransform': self.registrationResult.affineTransform.GetID(),
'outputVolume': self.registrationResult.affineVolume.GetID(),
'maskProcessingMode': "ROI",
'useAffine': True,
'initialTransform': self.registrationResult.rigidTransform}
slicer.cli.run(slicer.modules.brainsfit, None, paramsAffine, wait_for_completion=True)
self.registrationResult.cmdArguments += "Affine Registration Parameters: %s" % str(paramsAffine) + "\n\n"
def doBSplineRegistration(self, initialTransform, **kwargs):
self.updateProgress(labelText='\nBSpline registration', value=3)
paramsBSpline = {'fixedVolume': self.registrationResult.fixedVolume,
'movingVolume': self.registrationResult.movingVolume,
'outputVolume': self.registrationResult.bSplineVolume.GetID(),
'bsplineTransform': self.registrationResult.bSplineTransform.GetID(),
'fixedBinaryVolume': self.registrationResult.fixedLabel,
'movingBinaryVolume': self.registrationResult.movingLabel,
'useROIBSpline': True,
'useBSpline': True,
'splineGridSize': "3,3,3",
'maskProcessing': "ROI",
'minimumStepLength': "0.005",
'maximumStepLength': "0.2",
'costFunctionConvergenceFactor': "1.00E+09",
'maskProcessingMode': "ROI",
'initialTransform': initialTransform}
for key, value in kwargs.iteritems():
paramsBSpline[key] = value
slicer.cli.run(slicer.modules.brainsfit, None, paramsBSpline, wait_for_completion=True)
self.registrationResult.cmdArguments += "BSpline Registration Parameters: %s" % str(paramsBSpline) + "\n\n"
self.updateProgress(labelText='\nCompleted registration', value=4)
def updateProgress(self, **kwargs):
if self.progressCallback:
self.progressCallback(**kwargs)
